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Aliases for SALL1 Gene

Aliases for SALL1 Gene

  • Spalt Like Transcription Factor 1 2 3 5
  • Zinc Finger Protein Spalt-1 3 4
  • Zinc Finger Protein SALL1 3 4
  • Zinc Finger Protein 794 3 4
  • ZNF794 3 4
  • HSAL1 3 4
  • Sal-1 3 4
  • Epididymis Secretory Protein Li 89 3
  • Spalt-Like Transcription Factor 1 4
  • Sal (Drosophila)-Like 1 2
  • Sal-Like 1 (Drosophila) 2
  • Sal-Like Protein 1 3
  • HEL-S-89 3
  • SAL1 4
  • TBS 3

External Ids for SALL1 Gene

Previous HGNC Symbols for SALL1 Gene

  • TBS

Previous GeneCards Identifiers for SALL1 Gene

  • GC16M041583
  • GC16M050907
  • GC16M050948
  • GC16M049727
  • GC16M037057

Summaries for SALL1 Gene

Entrez Gene Summary for SALL1 Gene

  • The protein encoded by this gene is a zinc finger transcriptional repressor and may be part of the NuRD histone deacetylase complex (HDAC). Defects in this gene are a cause of Townes-Brocks syndrome (TBS) as well as bronchio-oto-renal syndrome (BOR). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for SALL1 Gene

SALL1 (Spalt Like Transcription Factor 1) is a Protein Coding gene. Diseases associated with SALL1 include Townes-Brocks Syndrome 1 and Townes-Brocks Syndrome. Among its related pathways are Transcriptional Regulatory Network in Embryonic Stem Cell and Developmental Biology. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and beta-catenin binding. An important paralog of this gene is SALL3.

UniProtKB/Swiss-Prot for SALL1 Gene

  • Transcriptional repressor involved in organogenesis.

Gene Wiki entry for SALL1 Gene

Additional gene information for SALL1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SALL1 Gene

Genomics for SALL1 Gene

GeneHancer (GH) Regulatory Elements for SALL1 Gene

Promoters and enhancers for SALL1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I051148 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 568.2 -0.3 -329 8.2 PKNOX1 FOXA2 ZFP64 ARID4B SIN3A FEZF1 ZNF48 YY1 GLIS2 FOS SALL1 ENSG00000261238 ENSG00000280344
GH16I051538 Enhancer 1.2 FANTOM5 Ensembl ENCODE 23.1 -387.4 -387378 2.7 FOXA2 INSM2 FEZF1 THRB RARA ZNF335 ZNF366 FOS TSHZ1 ZEB2 SALL1 LOC102723323 PIR35026
GH16I051542 Enhancer 1.3 VISTA UCNEbase ENCODE 12.1 -391.9 -391939 3.6 SP1 ZFHX2 GLIS1 ATF7 FEZF1 EGR2 SALL1 PIR35026 LOC102723323
GH16I051129 Enhancer 0.6 FANTOM5 22.2 +23.1 23092 0.3 ZSCAN4 ZNF580 KLF17 MAX HNF4A WT1 YY1 SALL1 LOC105371253 SOD1P2
GH16I051556 Enhancer 1.1 Ensembl ENCODE 7.8 -404.7 -404730 1.6 ARNT FEZF1 ZNF2 GLIS2 ZNF213 FOS REST TSHZ1 ZNF488 ZNF518A PIR35026 SALL1 HNRNPA1P48
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SALL1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SALL1 gene promoter:

Genomic Locations for SALL1 Gene

Genomic Locations for SALL1 Gene
16,342 bases
Minus strand

Genomic View for SALL1 Gene

Genes around SALL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SALL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SALL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SALL1 Gene

Proteins for SALL1 Gene

  • Protein details for SALL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sal-like protein 1
    Protein Accession:
    Secondary Accessions:
    • Q99881
    • Q9NSC3
    • Q9P1R0

    Protein attributes for SALL1 Gene

    1324 amino acids
    Molecular mass:
    140405 Da
    Quaternary structure:
    • Interacts with HDAC1, HDAC2, RBBP4, RBPP7, MTA1 and MTA2 (By similarity). Interacts with CCNQ. Probably associates with NuRD histone deacetylase complex (HDAC).

    Alternative splice isoforms for SALL1 Gene


neXtProt entry for SALL1 Gene

Post-translational modifications for SALL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SALL1 Gene

No data available for DME Specific Peptides for SALL1 Gene

Domains & Families for SALL1 Gene

Gene Families for SALL1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SALL1 Gene

Suggested Antigen Peptide Sequences for SALL1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the sal C2H2-type zinc-finger protein family.
  • Belongs to the sal C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with SALL1: view

Function for SALL1 Gene

Molecular function for SALL1 Gene

GENATLAS Biochemistry:
brain specific transcription factor,Drosophila homeotic gene Sal-like 1,expressed in corpus callosum and substantia nigra
UniProtKB/Swiss-Prot Function:
Transcriptional repressor involved in organogenesis.

Phenotypes From GWAS Catalog for SALL1 Gene

Gene Ontology (GO) - Molecular Function for SALL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0001078 transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding NAS 9425907
GO:0003700 DNA binding transcription factor activity IBA,NAS 9425907
genes like me logo Genes that share ontologies with SALL1: view
genes like me logo Genes that share phenotypes with SALL1: view

Human Phenotype Ontology for SALL1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SALL1 Gene

MGI Knock Outs for SALL1:

miRNA for SALL1 Gene

miRTarBase miRNAs that target SALL1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SALL1 Gene

Localization for SALL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SALL1 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SALL1 gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SALL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000792 heterochromatin IDA 15158448
GO:0005634 nucleus IEA,IDA 12065233
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IDA 12065233
GO:0010369 chromocenter IDA 16443351
genes like me logo Genes that share ontologies with SALL1: view

Pathways & Interactions for SALL1 Gene

genes like me logo Genes that share pathways with SALL1: view

Gene Ontology (GO) - Biological Process for SALL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 16443351
GO:0001657 ureteric bud development ISS --
GO:0001658 branching involved in ureteric bud morphogenesis ISS --
GO:0001822 kidney development IMP 16971658
GO:0003281 ventricular septum development ISS --
genes like me logo Genes that share ontologies with SALL1: view

No data available for SIGNOR curated interactions for SALL1 Gene

Drugs & Compounds for SALL1 Gene

(2) Drugs for SALL1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with SALL1: view

Transcripts for SALL1 Gene

Unigene Clusters for SALL1 Gene

Sal-like 1 (Drosophila):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SALL1 Gene

No ASD Table

Relevant External Links for SALL1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SALL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SALL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SALL1 Gene

This gene is overexpressed in Liver (x5.4), Brain - Spinal cord (cervical c-1) (x4.9), and Kidney - Cortex (x4.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SALL1 Gene

NURSA nuclear receptor signaling pathways regulating expression of SALL1 Gene:


SOURCE GeneReport for Unigene cluster for SALL1 Gene:


mRNA Expression by UniProt/SwissProt for SALL1 Gene:

Tissue specificity: Highest levels in kidney. Lower levels in adult brain (enriched in corpus callosum, lower expression in substantia nigra) and liver.

Evidence on tissue expression from TISSUES for SALL1 Gene

  • Liver(4.4)
  • Kidney(2.9)
  • Nervous system(2.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SALL1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • ear
  • eye
  • head
  • hypothalamus
  • neck
  • outer ear
  • pituitary gland
  • skull
  • thyroid
  • esophagus
  • heart
  • heart valve
  • lung
  • abdominal wall
  • biliary tract
  • duodenum
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • stomach
  • anus
  • pelvis
  • penis
  • rectum
  • testicle
  • ureter
  • urethra
  • urinary bladder
  • uterus
  • vagina
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
  • blood
  • blood vessel
  • coagulation system
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with SALL1: view

No data available for Protein differential expression in normal tissues and Protein tissue co-expression partners for SALL1 Gene

Orthologs for SALL1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SALL1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SALL1 33 34
  • 99.21 (n)
(Canis familiaris)
Mammalia SALL1 33 34
  • 91.07 (n)
(Monodelphis domestica)
Mammalia SALL1 34
  • 91 (a)
(Bos Taurus)
Mammalia SALL1 33 34
  • 90.09 (n)
(Rattus norvegicus)
Mammalia Sall1 33
  • 87.94 (n)
(Mus musculus)
Mammalia Sall1 33 16 34
  • 87.8 (n)
(Ornithorhynchus anatinus)
Mammalia SALL1 34
  • 84 (a)
(Gallus gallus)
Aves SALL1 33 34
  • 80.59 (n)
(Anolis carolinensis)
Reptilia SALL1 34
  • 80 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sall1 33
  • 74.28 (n)
Str.169 33
African clawed frog
(Xenopus laevis)
Amphibia MGC68418 33
(Danio rerio)
Actinopterygii sall1a 33 34
  • 68.8 (n)
Dr.14305 33
fruit fly
(Drosophila melanogaster)
Insecta salm 35 34
  • 62 (a)
salr 35 34
  • 35 (a)
(Caenorhabditis elegans)
Secernentea sem-4 34
  • 30 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes FZF1 34
  • 26 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 31 (a)
-- 34
  • 25 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4395 33
Species where no ortholog for SALL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SALL1 Gene

Gene Tree for SALL1 (if available)
Gene Tree for SALL1 (if available)

Paralogs for SALL1 Gene

Paralogs for SALL1 Gene Pseudogenes for SALL1 Gene

genes like me logo Genes that share paralogs with SALL1: view

Variants for SALL1 Gene

Sequence variations from dbSNP and Humsavar for SALL1 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs104894535 pathogenic, Townes-Brocks syndrome 1 51,141,107(-) G/C/T coding_sequence_variant, stop_gained
rs104894537 pathogenic, Townes-Brocks syndrome 1 51,141,396(-) G/A/T coding_sequence_variant, stop_gained, synonymous_variant
rs104894538 pathogenic, Townes-Brocks-branchiootorenal-like syndrome 51,141,255(-) G/A coding_sequence_variant, stop_gained
rs1064793257 pathogenic, not provided, Townes syndrome 51,138,807(-) AT/ coding_sequence_variant, frameshift
rs1085307143 pathogenic, Townes-Brocks syndrome 1 51,141,113(-) AC/ coding_sequence_variant, frameshift

Structural Variations from Database of Genomic Variants (DGV) for SALL1 Gene

Variant ID Type Subtype PubMed ID
dgv475n67 CNV gain 20364138
esv2658882 CNV deletion 23128226
nsv1066288 CNV gain 25217958
nsv833224 CNV loss 17160897
nsv952675 CNV deletion 24416366

Variation tolerance for SALL1 Gene

Residual Variation Intolerance Score: 11.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.07; 50.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SALL1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SALL1 Gene

Disorders for SALL1 Gene

MalaCards: The human disease database

(20) MalaCards diseases for SALL1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
townes-brocks syndrome 1
  • tbs1
townes-brocks syndrome
  • anus, imperforate, with hand, foot and ear anomalies
duane-radial ray syndrome
  • drrs
mosaic trisomy 8
  • mosaic trisomy chromosome 8
hemifacial microsomia
  • goldenhar syndrome with ipsilateral radial defect
- elite association - COSMIC cancer census association via MalaCards
Search SALL1 in MalaCards View complete list of genes associated with diseases


  • Townes-Brocks syndrome 1 (TBS1) [MIM:107480]: A form of Townes-Brocks syndrome, a rare autosomal dominant disease characterized by the triad of imperforate anus, dysplastic ears, and thumb malformations. Minor features of the condition include hearing loss, foot malformations, renal impairment with or without renal malformations, genitourinary malformations, and congenital heart disease. {ECO:0000269 PubMed:10533063, ECO:0000269 PubMed:9425907, ECO:0000269 PubMed:9973281}. Note=The disease is caused by mutations affecting the gene represented in this entry. Some individuals with SALL1 mutations manifest a phenotype overlapping with TBS1 and bronchio-oto-renal syndrome. Clinical features include dysplastic ears, hypoplastic kidneys with impaired renal function, gastroesophageal reflux, hypermetropia, hypospadias, and mild developmental delay. Affected individuals lack the characteristic anal or hand malformations of TBS1. {ECO:0000269 PubMed:10928856}.

Additional Disease Information for SALL1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SALL1: view

No data available for Genatlas for SALL1 Gene

Publications for SALL1 Gene

  1. Mutations in the SALL1 putative transcription factor gene cause Townes-Brocks syndrome. (PMID: 9425907) Kohlhase J … Engel W (Nature genetics 1998) 2 3 4 22 58
  2. A SALL1 mutation causes a branchio-oto-renal syndrome-like phenotype. (PMID: 10928856) Engels S … McGaughran J (Journal of medical genetics 2000) 3 4 22 58
  3. Molecular analysis of SALL1 mutations in Townes-Brocks syndrome. (PMID: 9973281) Kohlhase J … Engel W (American journal of human genetics 1999) 3 4 22 58
  4. Townes-Brocks syndrome: detection of a SALL1 mutation hot spot and evidence for a position effect in one patient. (PMID: 10533063) Marlin S … Petit C (Human mutation 1999) 3 4 22 58
  5. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 44 58

Products for SALL1 Gene

Sources for SALL1 Gene

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